On Thursday 20 November 2003 11:28, timothy driscoll wrote: > > > There is currently not a good mechanism in Jmol to support alternate > > > locations. Therefore, I will modify the .pdb reader to take the first > > > conformation it sees and discard the others. > > > > > > I have filed a bug report so that we don't lose the fact that we are > > > not supporting alternate conformations. > > hi Miguel, > > <cringe> I would put this fairly high on the priority list, actually. is > it just the semicolon that makes it difficult, or some larger issue?
The larger issue here is that Jmol does not have a way to represent alternative conformations right now... i.e. one way would be to store them as alternative frames... a sort of conformation animation... I'm not sure how the the script commands would trigger display one conformer over the other... I guess that one could even show combinatorial conformations based on conformations of each separate residue... right? In the latter case, it would require Jmol to mark an Atom with two coordinate sets... this is still doable, but Miguel and I need to have a very clear picture then what is intended... he's not a chemist, but I am, so I think we can work this out... even pretty quickly... So, my main question right now is, how do you use the alternative conformations of residues? Is there a webpage with Rasmol/Chime script, or some other demo that would examplify how the script commands are used and what effect they give... this will help me identify the best internal representation (one of the two options...)... > > This is the moment to repeat my description of already existing atom > > selecting primitives in RasMol 2.7.2 > > > > Primitive: [Gly]1:E.Ca;B/1 > > Residue name: Gly, ATP, [SO4], As? > > Residue number: 1,16,12,9-20 > > Insertion code: not implemented! > > Chain: :E > > Atom name: *.Ca, *.C??? > > Alternate location indicator: *;B (no wildcard) > > Model: */1 (no wildcards but /0) > > Wildcards: **:*.????/0 > > > > The Insertion code is really important and I'm very sad about the lack Do I understand correctly that the insertion code signals an alternative conformation? > of a primitive for it, but RasMol in contrary to Jmol > > is able to deal with it (there must be an internal primitive). What do you mean with an internal primitive... the data storage class, or a rasmol script command/identifier? > I am having trouble determining exactly what is the Insertion code? Me too... Egon -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
